Founder effect was the case of João Ramalho, a Portuguese Pioneer that
arrived in Brazil in 1510 and was the first European in São Paulo. The
Jesuits couldn't understand the Indian culture:

"In this land there is a João Ramalho. He has been here many years and his
life-style and that of his children is Indian and is a petra scandali for
us, because his life is a great hindrance for the Indians we have; he is
well known and well connected by kinship to the Indians. He has many women.
He and his sons have relations with sisters and have children by them....
They go to war with the Indians and their festivals are those of the Indians
and they live naked as the Indians"
36. Nóbrega to Câmara, 1553, in Leite, Novas cartas , 46.

Looks like founder effects at work Ricardo. You may be interested in this
article "Worldwide Distribution of a Polymorphic Alu Insertion in hte
Progesterone Receptor Gene" from this book "Genomic Diversity Applications
in Human Population Genetics".

The frequency of the PR Alu insertion is most frequent in Europe in the
Basque people. It is even more frequent in populations in the Yucatan (Maya
Buctzotz) and Northern Columbia as well as the Surui, Amazonia Brazil. After
these populations the frequency drops off substancially in other world
populations. It is absent in South/Central Asia and Sub Saharan Africa.

This paper says that some of the NA tribes involved in this study had been
isolated for some time suggesting a possible caucasian component in the
founders.